Hi Michael, we currently do not extract Gene Ontology data from Wikipedia.
We extract data for http://en.wikipedia.org/wiki/Template:Infobox_protein which doesn't use Gene Ontology. The template http://en.wikipedia.org/wiki/Template:GNF_Protein_box (and maybe others?) uses Gene Ontology, but we don't have a mapping from that template to our ontology (yet). Besides, most (if not all) of the IDs we already extract (ISBN, Protein Data Bank ID, etc.) are defined as strings, not as numbers, because with most of these, ranges and other numeric operations don't make sense. Would it actually make sense to search for genes annotated with a GO category "between" GO:0005488 and GO:0008047? Not sure what you mean by "descending from" and "2 hops from GO:0005488", but I guess the DBpedia extraction and/or the browser would have to use some kind of inference to enable such searches. There are other domains in which such inference would be useful (e.g., the browser doesn't know that someone who was born in Berlin was also born in Europe), so maybe one day we will implement it, but it's currently not high on our to-do list. Bye, Christopher On Thu, Oct 1, 2009 at 17:54, Grobe, David Michael <dgr...@iupui.edu> wrote: > Christopher: > > I suppose this is a different issue, but since you're "on the line", I'd like > to know if the interface supports searches on ontology ranges, so that I > could, for example, search for any gene annotated with any Gene Ontology > category "descending from" GO:0005488. or for any gene annotated with a GO > category "between" GO:0005488 and GO:0008047, or any gene within 2 hops from > GO:0005488, yada, yada. > > Thanks, > > :Michael > > > > >> -----Original Message----- >> From: Jona Christopher Sahnwaldt [mailto:jcsahnwa...@gmail.com] >> Sent: Monday, September 28, 2009 5:24 PM >> To: Richard Cyganiak; Grobe, David Michael >> Cc: dbpedia-discussion@lists.sourceforge.net >> Subject: Re: [Dbpedia-discussion] can't find Goethe using new faceted >> browser. >> >> Michael, Richard, >> >> you're correct, currently only the top values of each facet are used >> for auto suggestion, and the selected value must match exactly. >> When I find the time, I will extend the browser to use inexact >> matching for fields like 'name'. >> >> You can use the text search box at the top of the page to search >> for "Johann", though: >> >> http://dbpedia.neofonie.de/browse/~:Johann/ >> >> Johann Wolfgang von Goethe is the second result. >> >> >> Christopher >> >> On Mon, Sep 28, 2009 at 19:32, Richard Cyganiak <rich...@cyganiak.de> >> wrote: >> > On 28 Sep 2009, at 17:09, Grobe, David Michael wrote: >> >> But that's the strange part....Using the new browser, when I click >> >> "Person to filter by "Person", I get a list of predicates, including >> >> "name". Then when I enter "jo" in the "name" text field, a pull- >> >> down list of names appears, starting with "John", "John Davis", etc. >> >> >> >> If I enter "john r", I get a pull-down containing "John Russell(7) >> >> and John Reiley (6)", and if I actually enter "John Davis", I get a >> >> list with a single "John Davis (18)" entry, which I can select for >> >> the John Davis content... >> >> >> >> ....but "johann" gets me nothing...not even "Bach or Pachelbel". >> > >> > Ah, now I see what you mean. >> > >> > I think that the auto-completion in the facet fields just covers the >> > top N values for the facet. You find "John Russell" and "John Reiley" >> > because there are several entries with that value (that is, people >> > with that name -- 7 and 6, respectively). All the names that I can >> > find in the autocompletion dropdown, no matter what I enter, show at >> > least five people with that name, AFAICT. "Johann Wolfgang Goethe" >> > just occurs once, and so does not appear in the dropdown. >> > >> > I don't know if it's a bug. Sounds more like an intentional >> > restriction or limitation. >> > >> > It's still bad though, it would be much more useful if all facet >> > values were used for autocompletion. >> > >> > (I can't find Christopher's email address, so I'm CC'ing Christian >> > Becker, please forward it ;-) >> > >> > Best, >> > Richard >> > >> > >> > >> > >> >> >> >> Very odd; it's as if Goethe is not in the database, or maybe German >> >> names are not being processed (neither of which sound likely). >> >> >> >> :michael grobe >> >> >> >> >> >> >> >>> -----Original Message----- >> >>> From: Richard Cyganiak [mailto:rich...@cyganiak.de] >> >>> Sent: Sunday, September 27, 2009 6:27 AM >> >>> To: Grobe, David Michael >> >>> Cc: 'dbpedia-discussion@lists.sourceforge.net' >> >>> Subject: Re: [Dbpedia-discussion] can't find Goethe using new faceted >> >>> browser. >> >>> >> >>> Michael, >> >>> >> >>> On 26 Sep 2009, at 23:08, Grobe, David Michael wrote: >> >>>> I can't find Johann Wolfgang von Goethe using new faceted >> >>>> browser...starting with "Johan" in the Persons section, but I can >> >>>> find him by starting with birthdate... >> >>>> >> >>>> can someone tell me why? >> >>> >> >>> It seems you can find him by searching for "johann" or "goethe" in >> >>> the >> >>> persons section, but not searching for "johan", "jo" or "goet". >> >>> >> >>> I suppose the faceted browser does only exact matches on words, and >> >>> doesn't search for partial matches and doesn't correct misspellings. >> >>> >> >>> Best, >> >>> Richard >> >>> >> >>> >> >>>> >> >>>> thanks, >> >>>> >> >>>> michael grobe >> >>>> >> >>>> >> >>>> >> >>>> --------------------------------------------------------------------- >> --- >> >>> ------ >> >>>> Come build with us! The BlackBerry® Developer Conference in >> >>>> SF, CA >> >>>> is the only developer event you need to attend this year. Jumpstart >> >>>> your >> >>>> developing skills, take BlackBerry mobile applications to market and >> >>>> stay >> >>>> ahead of the curve. Join us from November 9-12, 2009. Register >> >>>> now! >> >>>> http://p.sf.net/sfu/devconf >> >>>> _______________________________________________ >> >>>> Dbpedia-discussion mailing list >> >>>> Dbpedia-discussion@lists.sourceforge.net >> >>>> https://lists.sourceforge.net/lists/listinfo/dbpedia-discussion >> >> >> > >> > >> > ------------------------------------------------------------------------ >> ------ >> > Come build with us! The BlackBerry® Developer Conference in SF, CA >> > is the only developer event you need to attend this year. Jumpstart your >> > developing skills, take BlackBerry mobile applications to market and >> stay >> > ahead of the curve. Join us from November 9-12, 2009. Register >> now! >> > http://p.sf.net/sfu/devconf >> > _______________________________________________ >> > Dbpedia-discussion mailing list >> > Dbpedia-discussion@lists.sourceforge.net >> > https://lists.sourceforge.net/lists/listinfo/dbpedia-discussion >> > > ------------------------------------------------------------------------------ Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf _______________________________________________ Dbpedia-discussion mailing list Dbpedia-discussion@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/dbpedia-discussion
